They're intended to be the Engineers, by all accounts. The crew referring to them as Deadgineers. The makeup difference is likely due to cost and effort of such a quick scene.
I am sure they also made an executive decision in production design that they might also look a bit different after 2,000 years. I doubt they were just uniformly comfortable not putting the same effort into the Engineer make up to save a few bucks.
The sacrificial engineer was potentially hundreds of millions of years before the incident on LV-223 and he wasn't made to be any different. They seem to be just fine not going through all the trouble of exactly replicating the Prometheus
engineers for a huge group of extras in what is a nonessential and likely split-second close up.
For all the fuss, they don't actually look terribly different. I think a lot of this comes from their funny expressions and how their faces aren't like greek statues.